The paper deals with computer simulation to achieve system optimization for warehouse management on a digital factory model. The Tecnomatix Plant Simulation program is used as a tool for a modern simulation environment. The case study realized two simulation experiments focusing on storage and optimizing storage warehouse processes. The study's experiments analyzed and solved mutual blockages of forklift trucks in shelf aisles and determined the optimal number of forklift trucks in the logistics system involved in loading and unloading trucks. Collisions between service and handling equipment in the aisles can restrict or block material flow from the warehouse to production. Therefore, it is necessary to change the arrangement of individual materials in the warehouse and determine the optimal number of service and handling equipment.